US20210382067A1 - High-throughput and mass-spectrometry-based method for quantitating antibodies - Google Patents

High-throughput and mass-spectrometry-based method for quantitating antibodies Download PDF

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US20210382067A1
US20210382067A1 US17/341,746 US202117341746A US2021382067A1 US 20210382067 A1 US20210382067 A1 US 20210382067A1 US 202117341746 A US202117341746 A US 202117341746A US 2021382067 A1 US2021382067 A1 US 2021382067A1
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antibody
sample
peptides
peptide
drug product
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Yuetian Yan
Shunhai Wang
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Regeneron Pharmaceuticals Inc
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Regeneron Pharmaceuticals Inc
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • G01N33/6857—Antibody fragments
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6848—Methods of protein analysis involving mass spectrometry
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/40—Fusion polypeptide containing a tag for immunodetection, or an epitope for immunisation
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2458/00—Labels used in chemical analysis of biological material
    • G01N2458/15—Non-radioactive isotope labels, e.g. for detection by mass spectrometry

Definitions

  • This invention is generally related to systems and methods for quantitating antibodies.
  • LC-MS/MS liquid chromatography coupled to tandem mass spectrometry
  • Liquid chromatography-free methods for quantitating a target protein in a sample are provided.
  • One embodiment provides a liquid chromatography-free method for quantifying target antibodies in a sample including the steps of spiking the sample with a labeled internal standard antibody, digesting the antibodies in the sample to produce peptides, fractionating the peptides; and quantifying the target antibodies using a direct infusion MS 2 system containing one or more ion traps and two or more quadrupole mass filters and an electrospray ionizer, wherein the method is liquid chromatography-free.
  • the method further includes the step of spiking the peptides with labeled Fc peptide VVSVLTVLHQDWLNGK (SEQ ID NO:1) prior to fractionation.
  • the peptides are fractionated by reverse phase solid phase extraction.
  • the labeled internal standard antibody and the labeled Fc peptide are typically labeled with a heavy isotope.
  • the heavy isotope is selected from the group consisting of 13 C, 15 N, and 2 H.
  • the target antibody is a human monoclonal antibody.
  • Still another embodiment provides a method of quantitating a protein drug product in a biological sample including the steps of spiking the sample with a known amount of a heavy isotope labeled peptide standard having an amino acid sequence according to SEQ ID NO:1, digesting protein drug product in the sample into peptides, fractionating the peptides under conditions that retain peptides having an amino acid sequence according to SEQ ID NO:1, analyzing the sample containing the protein drug product peptides and the peptide standards for the presence of the peptide having an amino acid sequence according to SEQ ID NO:1 using an MS 2 system to calibrate the system, wherein the MS 2 system comprises one or more ion traps and two or more quadrupole mass filters and an electrospray ionizer, and quantitating the amount of protein drug product present in the sample based upon the presence of the peptide, wherein the method does not utilize liquid chromatography.
  • the protein drug product can be an antibody or antigen binding fragment thereof, a fusion protein, or a recombinant protein.
  • the data for quantifying drug product ions and mass-tagged peptide standard ions are acquired in different MS 2 scans.
  • the peptides are fractionated using reverse phase solid phase extraction using 15 to 25% acetonitrile as a wash and 20 to 30% acetonitrile elution. In one embodiment, a 20% acetonitrile wash and 24% acetonitrile elution is used.
  • the method further includes the step of spiking the sample of protein drug product with a heavy isotope-labeled protein drug product prior to digesting the sample.
  • the sample contains blood or serum.
  • the blood or serum can be human or non-human. In one embodiment the serum is monkey serum.
  • the disclosed methods have a dynamic range of 1 to 1000 ⁇ m/mL and a Lower Limit of Quantification (LLOQ) of 1-2 ⁇ g/mL.
  • LLOQ Lower Limit of Quantification
  • the disclosed methods are automated high throughput methods.
  • FIG. 1 is a schematic illustration of the workflow of an exemplary method disclosed herein.
  • FIGS. 2A-2C are diagrams showing the workflow of exemplary methods disclosed herein.
  • FIGS. 3A-3F are exemplary graphs showing sequential parallel reaction monitoring (PRM) acquisition of endogenous and internal standard (IST) peptides.
  • FIGS. 4A-4C are exemplary graphs showing wide-range co-isolation of endogenous and IST peptides for PRM.
  • FIGS. 5A-5E are exemplary graphs showing 2-plexed PRM acquisition.
  • FIG. 6A is a mass spectrum graph of endogenous and spiked-in peptide y14++ acquired using wide isolation PRM at 1 ⁇ g/mL.
  • FIG. 6B is a mass spectrum graph of endogenous and spiked-in peptide y14++ acquired using 2-plexed PRM at 1 ⁇ g/mL.
  • FIG. 7A is a table showing the product ions tested in FIGS. 7B-7D .
  • FIGS. 7B-7E are mass spectra of endogenous and spiked-in y8+ and y14++ product ions in blank samples or 10 ⁇ g/mL samples of a mAb of interest.
  • FIG. 8A is a schematic diagram of the stepwise acetonitrile (ACN) gradient elution from an exemplary method disclosed herein.
  • FIG. 8B is a graph showing the VVSV peptide distribution percent across an ACN stepwise gradient.
  • FIG. 8C is a graph showing VVSV peptide intensity using different ACN elution windows (18% wash, 24% elute; 18% wash, 26% elute; 20% wash, 24% elute; 20% wash, 26% elute).
  • FIGS. 9A-9B are mass spectrum graphs showing relative abundance of y14++ product ion in an Oasis SPE plate washed with 18% ACN and eluted with 24% ACN ( FIG. 9A ) and in a Strata X-SPE plate washed with 20% ACN and eluted with 24% ACN.
  • FIGS. 10A-10B are calibration curves showing intensity of heavy peptide signal over various concentrations of heavy peptide. The data was fitted as a linear regression model with 1/x weighting.
  • FIGS. 11A-11B are calibration curves showing normalized response over various protein concentrations for samples spiked with heavy mAb internal standard. The data was fitted using a linear regression model with 1/x weighting.
  • FIG. 12 is a table showing QC sample analysis using the disclosed methods to detect antibody concentration.
  • FIGS. 13A-13B are mass spectrum graphs showing relative abundance of endogenous and SIL peptides in serum blank ( FIG. 13A ) and serum+internal standard mAb ( FIG. 13B ).
  • FIG. 14 is a table showing the determination of LLOQ using different lots of monkey serum.
  • FIG. 15A-15B are calibration curves showing relative response ( FIG. 15A ) and intensity ( FIG. 15B ) over various concentrations of mAb1 in monkey serum.
  • FIG. 15C is a table showing the results of QC sample analysis.
  • FIG. 16 is a bar graph showing that increased wash volume improves LLOQ.
  • the X-axis represents wash volume and the Y-axis represent response at 1 ⁇ g/mL mAb/blank.
  • Protein refers to a molecule comprising two or more amino acid residues joined to each other by a peptide bond. Protein includes polypeptides and peptides and may also include modifications such as glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, alkylation, hydroxylation and ADP-ribosylation. Proteins can be of scientific or commercial interest, including protein-based drugs, and proteins include, among other things, enzymes, ligands, receptors, antibodies and chimeric or fusion proteins.
  • Proteins are produced by various types of recombinant cells using well-known cell culture methods, and are generally introduced into the cell by genetic engineering techniques (e.g., such as a sequence encoding a chimeric protein, or a codon-optimized sequence, an intronless sequence, etc.) where it may reside as an episome or be integrated into the genome of the cell.
  • genetic engineering techniques e.g., such as a sequence encoding a chimeric protein, or a codon-optimized sequence, an intronless sequence, etc.
  • Antibody refers to an immunoglobulin molecule consisting of four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds.
  • Each heavy chain has a heavy chain variable region (HCVR or VH) and a heavy chain constant region.
  • the heavy chain constant region contains three domains, CH1, CH2 and CH3.
  • Each light chain has a light chain variable region and a light chain constant region.
  • the light chain constant region consists of one domain (CL).
  • the VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • the term “antibody” includes reference to both glycosylated and non-glycosylated immunoglobulins of any isotype or subclass.
  • the term “antibody” includes antibody molecules prepared, expressed, created or isolated by recombinant means, such as antibodies isolated from a host cell transfected to express the antibody.
  • the term antibody also includes bispecific antibody, which includes a heterotetrameric immunoglobulin that can bind to more than one different epitope. Bispecific antibodies are generally described in U.S. Pat. No. 8,586,713, which is incorporated by reference into this application.
  • Fc fusion proteins comprise part or all of two or more proteins, one of which is an Fc portion of an immunoglobulin molecule, which are not otherwise found together in nature. Preparation of fusion proteins comprising certain heterologous polypeptides fused to various portions of antibody-derived polypeptides (including the Fc domain) has been described, e.g., by Rath, T., et al., Crit Rev Biotech, 35(2): 235-254 (2015), Levin, D., et al., Trends Biotechnol, 33(1): 27-34 (2015)) “Receptor Fc fusion proteins” comprise one or more extracellular domain(s) of a receptor coupled to an Fc moiety, which in some embodiments comprises a hinge region followed by a CH2 and CH3 domain of an immunoglobulin. In some embodiments, the Fc-fusion protein comprises two or more distinct receptor chains that bind to one or more ligand(s). For example, an Fc-fusion protein is a trap, such as for example an IL
  • liquid chromatography-free means that the technique of liquid chromatography is not utilized in the disclosed methods and systems.
  • the protein drug product is an antibody or antigen-binding fragment thereof, a fusion protein, or a recombinant protein.
  • the antibody is typically a monoclonal antibody.
  • Accurate and reliable quantitation of protein drug product molecules in animal serum/plasma samples is critical to support toxicokinetic and pharmacokinetic studies during the development of protein-based and antibody-based therapeutics.
  • Another embodiment provides high-throughput systems and methods including a liquid chromatograph-free (LC-free), parallel reaction monitoring (PRM)-based mass spectrometry (MS) method for quantitating mAbs, typically human antibodies, in a sample ( FIG. 1 ).
  • LC-free liquid chromatograph-free
  • PRM parallel reaction monitoring
  • MS mass spectrometry
  • Another embodiment provides a method utilizing nano-spray based direct infusion for high throughput analysis ( ⁇ 1 min per sample, zero cross-run contamination) and a universal surrogate peptide (VVSVLTVLHQDWLNGK (SEQ ID NO:1)) from the Fc region as an internal control for total human mAb quantitation in a sample.
  • VVSVLTVLHQDWLNGK SEQ ID NO:1
  • An exemplary liquid chromatography-free method includes digesting the protein sample into peptides, spiking in a heavy isotope labelled-peptide standard having the amino acid sequence of the surrogate peptide such as SEQ ID NO:1, fractionating the sample, and analyzing the sample using a direct infusion MS system containing one or more ion traps, two or more quadrupole mass filters, and an electrospray ionizer ( FIG. 2A ).
  • Still another embodiment provides a liquid chromatography-free method for quantifying antibody concentration in a sample including the steps of spiking the sample with an internal standard, for example a labeled antibody, digesting the antibodies in the sample to produce peptides, separating the peptides, for example using solid phase extraction, and quantifying the amount of antibody in the sample using a direct infusion MS system.
  • the direct infusion MS system includes one or more ion traps, two or more quadrupole mass filters, and an electrospray ionizer ( FIG. 2B ).
  • Yet another embodiment provides a liquid chromatography-free method for quantifying target antibodies in a sample including the steps of spiking the sample with a labeled standard antibody, digesting the antibodies in the sample to produce peptides, fractionating the peptides, and quantifying the target antibodies using a direct infusion MS system containing one or more ion traps and two or more quadrupole mass filters and an electrospray ionizer ( FIG. 2C ).
  • the protein or protein drug product of interest for example an antibody or antigen-binding fragment thereof, fusion protein, or a recombinant protein
  • a labelled internal standard peptide for example SEQ ID NO:1 is spiked into the sample containing target antibodies, and then the sample is subjected to protein digestion.
  • the sample containing the target antibodies is spiked with a labeled standard antibody and then subjected to digestion.
  • Proteins can be digested by enzymatic digestion with proteolytic enzymes or by non-enzymatic digestion with chemicals.
  • exemplary proteolytic enzymes for digesting proteins include but are not limited to trypsin, pepsin, chymotrypsin, thermolysin, papain, pronase, Arg-C, Asp-N, Glu-C, Lys-C, and Lys-N. Combinations of proteolytic enzymes can be used to ensure complete digestion.
  • Exemplary chemicals for digesting proteins include but are not limited to formic acid, hydrochloric acid, acetic acid, cyanogen bromide, 2-nitro-5-thiocyanobenzoate, and hydroxylamine.
  • the digestion step of the method is performed using 96 well plates in the Biomek® FXP Automated Workstation from Beckman Coulter which provides the speed and performance critical to today's research environments.
  • the flexible platform is available in single and dual pipetting head models combining multichannel (96 or 384) and Span-8 pipetting, and is ideal for high throughput workflows.
  • the sample is diluted with 8 M urea, trypsinized overnight at a ratio of 1 to 10 under reduced conditions.
  • exemplary reducing agents include 2-Mercaptoethanol and Dithiothreitol (DTT).
  • DTT Dithiothreitol
  • the sample is reduced with 10 mM DTT.
  • the sample is subject to fractionation to separate the digested peptides.
  • the sample is fractionated under conditions that allow for the retention of the internal standard peptide (VVSVLTVLHQDWLNGK; (SEQ ID NO:1)) and removal of the majority of other interferences for improved method sensitivity.
  • the fractionation is performed using solid phase extraction, in particular reverse phase solid phase extraction in a 96 well plate.
  • Solid phase extraction (SPE) parameters were explored by comparing several commercially available SPE products including Oasis HLB reverse phase 30 mg plate, Oasis HLB reverse phase 10 mg plate, Strata-X reverse phase 10 mg plate, Strata-X reverse phase 2 mg plate, Strata-XC strong cation exchange mix mode plate, and the Strata-XA strong Anion exchange mix mode plate.
  • FIG. 8A shows the stepwise elution profile.
  • FIG. 8C shows the internal control peptide intensity determined by mass spectrometry analysis under the indicated wash and elute concentrations of ACN. A 20% ACN wash with a 24% ACN elution was determined to be optimal.
  • FIG. 9A Comparison of elution profiles between Oasis HLB reverse phase 10 mg 96 plate ( FIG. 9A ) and Strata-X reverse phase 10 mg plate ( FIG. 9B ) was also performed.
  • the data show that the 2 mg Strata-X reverse phase plate provided the strongest signal of 6.31E3 ( FIG. 9B ).
  • Table 1 shows exemplary SPE parameters for fractionating the digested samples.
  • the fractionated peptides are quantified using a mass spectrometry system containing one or more ion traps and one or more hybrid quadrupole mass filters equipped with an electrospray ionizer.
  • An exemplary mass spectrometry system includes, but is not limited to a Thermo Q ExactiveTM Plus mass spectrometer in PRM mode equipped with a TriVersa NanoMate® system for initiating nanospray ionization.
  • This system has advanced quadrupole technology (AQT) that improves precursor selection and transmission for more-accurate quantitation of low-abundance analytes in complex matrices.
  • the system also has sophisticated data-independent acquisition (DIA) and parallel reaction monitoring (PRM) to deliver reproducible quantitation with complete qualitative confidence.
  • AABG advanced active beam guide
  • quantification data is acquired using sequential PRM acquisition of endogenous and IST peptides.
  • 2-plexed PRM acquisition is used.
  • the data for quantifying product ions are acquired in different MS 2 scans.
  • the MS 2 is calibrated using a heavy isotope labeled internal standard peptide VVSVLTVLHQDWLNGK (SEQ ID NO:1).
  • the internal standard peptide is labeled with a 13 C, 15 N, and 2 H, for example one or more Lys residues can be labeled with the isotope.
  • SEQ ID NO:1 is present in all human IgG isotypes and can be reliably produced from enzyme digestion. The sequence cannot be found in any other animal species and has good MS ionization efficiency.
  • the internal standard peptide is spiked into the sample to be analyzed prior to or concurrent with digestion of the proteins in the sample.
  • FIGS. 10A and 10B show calibration curves using SEQ ID NO:1.
  • the HCD collision energy for MS 2 analysis is calibrated using a heavy isotope labeled internal standard peptide to achieve the best signal intensity for the fragment ion intended for quantitation use.
  • the MS 2 system is calibrated using an antibody labeled with a heavy isotope or a mass tag.
  • the heavy isotope is selected from the group consisting of 13 C, 15 N, and 2 H.
  • An exemplary internal standard antibody is labeled with C 13 and N 15 on one or more Lys residues.
  • a SILuTMMAB Stable-Isotope Labeled Universal Monoclonal Antibody Standard (human) can be used.
  • FIGS. 11A and 11B show calibration curves using the labeled internal standard antibody.
  • FIG. 13A is a scan of a blank and 13 B shows a scan with the internal standard in the blank.
  • FIG. 13A one lot of monkey serum was digested by Trypsin and followed by offline SPE clean up. Then analyzed by MS using PRM method. The signal for the internal standard is very low (4.27E2).
  • FIG. 13B 10 ⁇ g/mL of the internal standard was spiked into monkey serum and then digested by Trypsin and followed by offline SPE clean up. Then analyzed by MS using PRM method. As you can see the signal for the internal standard is 1.97E4. This experiment shows the blank monkey serum is free of interference for internal standard.
  • FIG. 12 describes the data obtained from quality control analysis.
  • 4 levels of NISTmAb, Humanized IgG1k Monoclonal Antibody (Sigma-Aldrich) were spiked into monkey serum from 1 to 600 ⁇ g/mL.
  • 6 samples were prepared independently. All samples were digested by Trypsin and cleaned up by SPE. All samples were analyzed by MS. Based on the calibration curve, the detected concentration was calculated. The accuracy was calculated by using the average detected concentration divided by nominal concentration. The precision was calculated using the % relative standard deviation (RSD) of 6 samples at each level.
  • RSD % relative standard deviation
  • FIG. 14 shows the determination of the Lower Limit of Quantification (LLOQ) using different lots of monkey blood.
  • LLOQ Lower Limit of Quantification
  • FIG. 15A shows the calibration curve generated in this method. Different concentration of NISTmAb from 1 ⁇ g/mL to 1000 ⁇ g/mL were spiked into monkey serum, and each sample was then spiked with 10 ⁇ g/mL of internal standard and followed by trypsin digestion and SPE clean up. All samples were analyzed by MS. The intensity of each sample was normalized using IS and then plotted with nominal concentration.
  • FIG. 15B shows the zoomed region from 1 ⁇ g/mL to 50 ⁇ g/mL. As shown, the curve fits all points well in the low concentration range.
  • FIG. 15C shows similar data as FIG. 12 . The only difference is that mAb1 was used instead of NISTmAb here. mAb1 is an IgG4, and NISTmAb is a IgG1. The data show this method is suitable for both IgG1 and IgG4.
  • FIG. 16 is a bar graph showing that increased wash volume improves LLOQ.
  • the X-axis represents wash volume and the Y-axis represent response at 1 ⁇ g/mL mAb/blank.
  • the data show that increasing the wash volume during the SPE can improve the LLOD.
  • 1 ⁇ g/mL of NISTmAb was spiked into monkey serum and the sample was digested with trypsin. During the SPE step, the plate was washed with different volumes of wash buffer while keeping the other procedure the same.
  • the wash volume was increase from 100 ⁇ L to 600 the ratio of the response in the sample compared with blank increased from below 4 to over 6. The ratio should be at least 5 for the LLOD based on the requirement of method qualification from FDA. So by increasing the wash volume, the LLOD was improved to 1 ⁇ g/mL.
  • the protein of interest is a protein drug product or is a protein of interest suitable for expression in prokaryotic or eukaryotic cells.
  • the protein can be an antibody or antigen-binding fragment thereof, a chimeric antibody or antigen-binding fragment thereof, an ScFv or fragment thereof, an Fc-fusion protein or fragment thereof, a growth factor or a fragment thereof, a cytokine or a fragment thereof, or an extracellular domain of a cell surface receptor or a fragment thereof.
  • Proteins in the complexes may be simple polypeptides consisting of a single subunit, or complex multi-subunit proteins comprising two or more subunits.
  • the protein of interest may be a biopharmaceutical product, food additive or preservative, or any protein product subject to purification and quality standards
  • the protein of interest is an antibody, a human antibody, a humanized antibody, a chimeric antibody, a monoclonal antibody, a multispecific antibody, a bispecific antibody, an antigen binding antibody fragment, a single chain antibody, a diabody, triabody or tetrabody, a dual-specific, tetravalent immunoglobulin G-like molecule, termed dual variable domain immunoglobulin (DVD-IG), an IgD antibody, an IgE antibody, an IgM antibody, an IgG antibody, an IgG1 antibody, an IgG2 antibody, an IgG3 antibody, or an IgG4 antibody.
  • the antibody is an IgG1 antibody.
  • the antibody is an IgG2 antibody. In one embodiment, the antibody is an IgG4 antibody. In another embodiment, the antibody comprises a chimeric hinge. In still other embodiments, the antibody comprises a chimeric Fc. In one embodiment, the antibody is a chimeric IgG2/IgG4 antibody. In one embodiment, the antibody is a chimeric IgG2/IgG1 antibody. In one embodiment, the antibody is a chimeric IgG2/IgG1/IgG4 antibody.
  • the antibody is selected from the group consisting of an anti-Programmed Cell Death 1 antibody (e.g., an anti-PD1 antibody as described in U.S. Pat. Appln. Pub. No. US2015/0203579A1), an anti-Programmed Cell Death Ligand-1 (e.g., an anti-PD-L1 antibody as described in in U.S. Pat. Appln. Pub. No. US2015/0203580A1), an anti-DLL4 antibody, an anti-Angiopoetin-2 antibody (e.g., an anti-ANG2 antibody as described in U.S. Pat. No.
  • an anti-Programmed Cell Death 1 antibody e.g., an anti-PD1 antibody as described in U.S. Pat. Appln. Pub. No. US2015/0203579A1
  • an anti-Programmed Cell Death Ligand-1 e.g., an anti-PD-L1 antibody as described in in U.S. Pat. Appln. Pub. No. US2015/
  • an anti-Angiopoetin-Like 3 antibody e.g., an anti-AngPt13 antibody as described in U.S. Pat. No. 9,018,356
  • an anti-platelet derived growth factor receptor antibody e.g., an anti-PDGFR antibody as described in U.S. Pat. No. 9,265,827
  • an anti-Erb3 antibody e.g., an anti-Prolactin Receptor antibody as described in U.S. Pat. No. 9,302,015
  • an anti-Complement 5 antibody e.g., an anti-CS antibody as described in U.S. Pat. Appln. Pub.
  • an anti-TNF antibody an anti-epidermal growth factor receptor antibody (e.g., an anti-EGFR antibody as described in U.S. Pat. No. 9,132,192 or an anti-EGFRvIII antibody as described in U.S. Pat. Appln. Pub. No. US2015/0259423A1)
  • an anti-Proprotein Convertase Subtilisin Kexin-9 antibody e.g., an anti-PCSK9 antibody as described in U.S. Pat. No. 8,062,640 or 9,540,449
  • an Anti-Growth and Differentiation Factor-8 antibody e.g. an anti-GDF8 antibody, also known as anti-myostatin antibody, as described in U.S.
  • an anti-Glucagon Receptor e.g. anti-GCGR antibody as described in U.S. Pat. Appln. Pub. Nos. US2015/0337045A1 or US2016/0075778A1
  • an anti-VEGF antibody e.g., an anti-IL1R antibody
  • an interleukin 4 receptor antibody e.g., an anti-IL4R antibody as described in U.S. Pat. Appln. Pub. No. US2014/0271681A1 or U.S. Pat. No. 8,735,095 or 8,945,559
  • an anti-interleukin 6 receptor antibody e.g., an anti-IL6R antibody as described in U.S. Pat. No.
  • an anti-IL1 antibody an anti-IL2 antibody, an anti-IL3 antibody, an anti-IL4 antibody, an anti-IL5 antibody, an anti-IL6 antibody, an anti-IL7 antibody, an anti-interleukin 33 (e.g., anti-IL33 antibody as described in U.S. Pat. No. 9,453,072 or 9,637,535), an anti-Respiratory syncytial virus antibody (e.g., anti-RSV antibody as described in U.S. Pat. No. 9,447,173), an anti-Cluster of differentiation 3 (e.g., an anti-CD3 antibody, as described in U.S. Pat. Nos.
  • an anti-Cluster of differentiation 20 e.g., an anti-CD20 antibody as described in U.S. Pat. No. 9,657,102 and US20150266966A1, and in U.S. Pat. No. 7,879,984
  • an anti-CD19 antibody, an anti-CD28 antibody, an anti-Cluster of Differentiation-48 e.g. anti-CD48 antibody as described in U.S. Pat. No. 9,228,01
  • an anti-Fel d1 antibody e.g. as described in U.S. Pat. No. 9,079,948
  • an anti-Middle East Respiratory Syndrome virus e.g.
  • an anti-MERS antibody as described in U.S. Pat. Appln. Pub. No. US2015/0337029A1
  • an anti-Ebola virus antibody e.g. as described in U.S. Pat. Appln. Pub. No. US2016/0215040
  • an anti-Zika virus antibody e.g. an anti-LAG3 antibody, or an anti-CD223 antibody
  • an anti-Nerve Growth Factor antibody e.g. an anti-NGF antibody as described in U.S. Pat. Appln. Pub. No. US2016/0017029 and U.S. Pat. Nos. 8,309,088 and 9,353,176
  • an anti-Protein Y antibody e.g. an anti-MERS antibody as described in U.S. Pat. Appln. Pub. No. US2015/0337029A1
  • an anti-Ebola virus antibody e.g. as described in U.S. Pat. Appln. Pub. No. US2016/0215040
  • the bispecific antibody is selected from the group consisting of an anti-CD3 ⁇ anti-CD20 bispecific antibody (as described in U.S. Pat. Appln. Pub. Nos. US2014/0088295A1 and US20150266966A1), an anti-CD3 ⁇ anti-Mucin 16 bispecific antibody (e.g., an anti-CD3 ⁇ anti-Muc16 bispecific antibody), and an anti-CD3 ⁇ anti-Prostate-specific membrane antigen bispecific antibody (e.g., an anti-CD3 ⁇ anti-PSMA bispecific antibody).
  • an anti-CD3 ⁇ anti-CD20 bispecific antibody as described in U.S. Pat. Appln. Pub. Nos. US2014/0088295A1 and US20150266966A1
  • an anti-CD3 ⁇ anti-Mucin 16 bispecific antibody e.g., an anti-CD3 ⁇ anti-Muc16 bispecific antibody
  • an anti-CD3 ⁇ anti-Prostate-specific membrane antigen bispecific antibody e.g.
  • the protein of interest is selected from the group consisting of abciximab, adalimumab, adalimumab-atto, ado-trastuzumab, alemtuzumab, alirocumab, atezolizumab, avelumab, basiliximab, belimumab, benralizumab, bevacizumab, bezlotoxumab, blinatumomab, brentuximab vedotin, brodalumab, canakinumab, capromab pendetide, certolizumab pegol, cemiplimab, cetuximab, denosumab, dinutuximab, dupilumab, durvalumab, eculizumab, elotuzumab, emicizumab-kxwh, emtansinealirocumab
  • the protein of interest is a recombinant protein that contains an Fc moiety and another domain (e.g., an Fc-fusion protein).
  • an Fc-fusion protein is a receptor Fc-fusion protein, which contains one or more extracellular domain(s) of a receptor coupled to an Fc moiety.
  • the Fc moiety comprises a hinge region followed by a CH2 and CH3 domain of an IgG.
  • the receptor Fc-fusion protein contains two or more distinct receptor chains that bind to either a single ligand or multiple ligands.
  • an Fc-fusion protein is a TRAP protein, such as for example an IL-1 trap (e.g., rilonacept, which contains the IL-1RAcP ligand binding region fused to the Il-1R1 extracellular region fused to Fc of hIgG1; see U.S. Pat. No. 6,927,004, which is herein incorporated by reference in its entirety), or a VEGF trap (e.g., aflibercept or ziv-aflibercept, which comprises the Ig domain 2 of the VEGF receptor Flt1 fused to the Ig domain 3 of the VEGF receptor Flk1 fused to Fc of hIgG1; see U.S. Pat. Nos.
  • IL-1 trap e.g., rilonacept, which contains the IL-1RAcP ligand binding region fused to the Il-1R1 extracellular region fused to Fc of hIgG1; see U.S. Pat. No. 6,927,
  • an Fc-fusion protein is a ScFv-Fc-fusion protein, which contains one or more of one or more antigen-binding domain(s), such as a variable heavy chain fragment and a variable light chain fragment, of an antibody coupled to an Fc moiety.
  • Calibration standards (1, 2.5, 5, 10, 25, 50, 100, 250, 500 and 1000 ⁇ g/mL) and quality controls (QCs) (1, 3, 60 and 600 ⁇ g/mL) were prepared from the stock solutions of NISTmAb (10 mg/mL) by serial dilutions with control monkey serum.
  • QCs quality controls
  • two laboratory quality control (LQC) samples were each prepared for six different lots of blank monkey serum by spiking in NISTmAb, a humanized IgG1k monoclonal antibody, at 1 ⁇ g/mL and 2 ⁇ g/mL. 20 ⁇ L of each standard sample was spiked with 200 ng of heavy isotope labeled mAb (IS-mAb) before subjecting to trypsin digestion.
  • IS-mAb heavy isotope labeled mAb
  • Each sample was denatured, reduced and digested with trypsin for overnight followed by cleaning up using a 96 well solid phase extraction (SPE) plate.
  • SPE solid phase extraction
  • the SPE wash and elution conditions were optimized to retain the target peptide (VVSVLTVLHQDWLNGK; (SEQ ID NO:1)) and remove majority of other interferences for improved method sensitivity.
  • Each sample was introduced to MS analysis on a Thermo Q Exactive Plus mass spectrometer in PRM mode equipped with a TriVersa NanoMate system for initiating nanospray ionization. Data was acquired using a multiplexed PRM method lasting 45 seconds for each sample.
  • the Fc peptide VVSVLTVLHQDWLNGK (SEQ ID NO:1) was chosen because of its good MS sensitivity, presence in two human IgG subclasses (IgG1 and IgG4) commonly used in antibody therapeutics, and absence in non-human IgGs from all commonly used animal species.
  • the trypsin digestion conditions, SPE conditions, PRM parameters, and fragment ion choice were all optimized.
  • the SPE condition was essential to removing most interferences while retaining majority of the surrogate peptide.
  • the PRM parameters and fragment ion choice were key to good data accuracy and method sensitivity.
  • this LC-free PRM-MS based method has demonstrated to be suitable for high-throughput and generic quantitation of humanized therapeutic mAbs in animal serum with a quantitation range of 2-1000 ⁇ g/mL.

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